scripts/deep_docs/fetch_parse.py

#!/usr/bin/env python3
"""
fetch_parse.py — fetch & text-extract the CDS/ADS/EWDS deep documentation
(Confluence wiki pages + PDFs + service webpages) so the non-marine stores get
the same deep-doc RAG depth as CMEMS marine.

Input : meta_harvest/deep_doc_plan.json   dataset_id -> [{title,url,kind}]
Output: deep_docs/parsed/<urlhash>.md     cleaned text per unique URL
        deep_docs/manifest.jsonl          one line per URL (checkpoint: resumable)

No VLM needed: Confluence/webpages via requests+bs4+markdownify, PDFs via PyMuPDF.
Env: SAMPLE_N=<n> to only process the first n URLs (smoke test).
"""
import json
import os
import re
import sys
import hashlib
import threading
from concurrent.futures import ThreadPoolExecutor, as_completed
from pathlib import Path

import requests
from bs4 import BeautifulSoup
from markdownify import markdownify as mdify
import fitz  # PyMuPDF

ROOT = Path(__file__).resolve().parent.parent
PLAN = ROOT / "meta_harvest" / "deep_doc_plan.json"
OUTDIR = ROOT / "deep_docs" / "parsed"
MANIFEST = ROOT / "deep_docs" / "manifest.jsonl"
UA = {"User-Agent": "Mozilla/5.0 (copernicus-rag deep-doc harvester; research use)"}


def log(*a):
    print(*a, file=sys.stderr, flush=True)


def uhash(url):
    return hashlib.md5(url.encode()).hexdigest()[:16]


def clean_md(md: str) -> str:
    md = re.sub(r"\n{3,}", "\n\n", md)
    md = re.sub(r"[ \t]+\n", "\n", md)
    # drop obvious confluence chrome lines
    drop = ("Skip to", "Configure Space tools", "Space shortcuts", "Copyright ©",
            "Powered by Atlassian", "Evaluate Confluence", "You are viewing")
    lines = [ln for ln in md.splitlines() if not any(d in ln for d in drop)]
    return "\n".join(lines).strip()


def parse_html(html: str) -> str:
    soup = BeautifulSoup(html, "html.parser")
    for t in soup(["script", "style", "nav", "header", "footer", "noscript", "form"]):
        t.decompose()
    node = (soup.select_one("#main-content") or soup.select_one(".wiki-content")
            or soup.select_one("div[role=main]") or soup.select_one("main")
            or soup.select_one("article") or soup.body or soup)
    md = mdify(str(node), heading_style="ATX", strip=["img"])
    return clean_md(md)


def parse_pdf(content: bytes) -> str:
    doc = fitz.open(stream=content, filetype="pdf")
    parts = [page.get_text("text") for page in doc]
    doc.close()
    return clean_md("\n\n".join(parts))


def fetch_one(url: str, kind: str) -> tuple[str, str]:
    """Return (markdown, status). status in {ok, empty, http_<code>, error}."""
    try:
        r = requests.get(url, headers=UA, timeout=40, allow_redirects=True)
        if r.status_code != 200:
            return "", f"http_{r.status_code}"
        ct = r.headers.get("content-type", "").lower()
        if kind == "pdf" or "application/pdf" in ct or url.lower().split("?")[0].endswith(".pdf"):
            md = parse_pdf(r.content)
        else:
            md = parse_html(r.text)
        return md, ("ok" if len(md) >= 200 else "empty")
    except Exception as e:
        return "", f"error:{type(e).__name__}"


def main():
    OUTDIR.mkdir(parents=True, exist_ok=True)
    plan = json.loads(PLAN.read_text())
    # unique url -> {title, kind, datasets:[]}
    urls: dict[str, dict] = {}
    for dsid, docs in plan.items():
        for d in docs:
            u = d["url"]
            e = urls.setdefault(u, {"title": d.get("title", ""), "kind": d.get("kind"), "datasets": []})
            e["datasets"].append(dsid)

    done = set()
    if MANIFEST.exists():
        for line in MANIFEST.read_text().splitlines():
            if line.strip():
                done.add(json.loads(line)["url"])
    todo = [u for u in urls if u not in done]
    sample = int(os.environ.get("SAMPLE_N", "0"))
    if sample:
        todo = todo[:sample]
    log(f"unique urls={len(urls)} done={len(done)} todo={len(todo)}"
        + (f" (SAMPLE {sample})" if sample else ""))

    workers = int(os.environ.get("WORKERS", "10"))
    lock = threading.Lock()
    counts = {"ok": 0, "done": 0}
    mf = open(MANIFEST, "a", encoding="utf-8")

    def work(url):
        meta = urls[url]
        md, status = fetch_one(url, meta["kind"])
        rec = {"url": url, "kind": meta["kind"], "title": meta["title"],
               "datasets": meta["datasets"], "status": status,
               "n_chars": len(md), "md_path": ""}
        if status == "ok":
            p = OUTDIR / f"{uhash(url)}.md"
            header = f"# {meta['title']}\n\n<!-- source: {url} -->\n\n"
            p.write_text(header + md, encoding="utf-8")
            rec["md_path"] = str(p.relative_to(ROOT))
        with lock:
            mf.write(json.dumps(rec, ensure_ascii=False) + "\n")
            mf.flush()
            counts["done"] += 1
            counts["ok"] += status == "ok"
            if counts["done"] % 40 == 0:
                log(f"  {counts['done']}/{len(todo)}  ok={counts['ok']}")

    with ThreadPoolExecutor(max_workers=workers) as ex:
        list(as_completed(ex.submit(work, u) for u in todo))
    mf.close()
    log(f"DONE todo={len(todo)} ok={counts['ok']}")


if __name__ == "__main__":
    main()